Comments (9)
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>&2 echo Removing adapters | /pipeline_tools/adapterremoval/AdapterRemoval --file1 /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/0_sorted_raw_input/pair_1_sorted.fastq --file2 /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/0_sorted_raw_input/pair_2_sorted.fastq --qualitybase 33 --threads 80 --minlength 30 --basename /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal_AdapterRemoval --trimqualities --output1 /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal/pair_1_adptr_rem.fastq --output2 /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal/pair_2_adptr_rem.fastq --singleton /scratch/j/jparkin/billyc59/Humann2_benchmark_run/rna_synth/quality_filter/data/1_adapter_removal/singletons_adptr_rem.fastq
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Threads: What are the parallelism limits on this program? I am using an 80-thread core machine to run your program.
outputs: yes, pair_1_adptr_rem.fastq, pair_2_adptr_rem.fastq and singletons_adptr_rem.fastq are completely blank.
Are they blank for you too?
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from adapterremoval.
version: version 2.1.7. Is there a newer one?
Oh, I see. it's a malformed header
Trimming paired end reads ... Error reading FASTQ record at line 1; aborting: Malformed or empty FASTQ header
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I don't really understand this error.
Does this program need "/1" and "/2" at the end of each fastq ID for paired-end mode?
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from adapterremoval.
The fault is with my own code, and not an issue with yours. Thank you again for your help.
My particular issue is due to a Pandas import error making a mess of my input file.
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Related Issues (20)
- --combined-output generates strange GC% distribution in fastqc reports HOT 4
- stdout and stderr reversed? HOT 1
- homebrew/science was deprecated HOT 1
- Adapter Removal running error HOT 2
- Internal barcodes HOT 5
- Support JSON log output HOT 3
- Add option for singular 'combined' output FASTQ files HOT 5
- Input file is overwritten and cut off HOT 3
- Adapters Not Being Trimmed (Apparently)? HOT 2
- collapse with SE reads HOT 3
- How to demultiplexing paired-end reads in mixed orientation? HOT 4
- installation Adapterremoval with Conda HOT 2
- AdapterRemoval v3 Feedback HOT 12
- remove adapters sequences from BGI/MGI platform HOT 1
- combine with other QC tools HOT 1
- How to interpret the outputs of the multiple inputs after trimming? HOT 4
- New version of catch.hpp needed for glibc >= 2.34 HOT 1
- [feature request] Add support for GNU make's staged install via DESTDIR flag HOT 1
- support .gz format fastq as input HOT 1
- adapterremoval add windows version HOT 2
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